I agree with you! But Illumina looked at the run and they said the parameters are still acceptable.

It is interesting if they actually said that. Perhaps they did not want to spook you

Quote:

Our bioinformatician said "The 3’-end quality is quite poor for both the R1 and R2 and there are strong 3’-end sequence biases".
Why is the quality poor on 3'-end? Any explanation?

That is to be expected. When a run is overclustered the clusters are very close to begin with. Over the run they become fatter and then the software has a tough time telling them apart. You could easily lose a run due to this. In your case though since this is mix of genomic DNA's the run was able to end successfully but the Q-scores suffered when the reliability of basecalls dropped towards the end of the run.